I wouldn't prefer this, because if "colour note heads by pitch" becomes an option, this would overlap the coloured note head and reduce the functionality. Also, in my view, a selection should draw the eye - overlaying the note heads this way actually makes them closer to the value of the background, reducing contrast and making them less visible, in terms of readability, compared to surrounding unselected notes.

But I do agree it would be neater than the current implementation. I'm just throwing out alternatives too!

I see yes, maybe just surrounding the current note with a square or something. But for example in Sibelius when you select a note it's colored blue, and it's handy and easy to see what's actually selected.